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Open data
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Basic information
Entry | Database: PDB / ID: 7ujj | ||||||
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Title | Stx2a and DARPin complex | ||||||
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![]() | ANTITOXIN / DARPin / shiga toxin | ||||||
Function / homology | ![]() modulation of host virulence by virus / hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region Similarity search - Function | ||||||
Biological species | Synthetic construct (others)![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||
![]() | Jiang, M. / Zhang, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Multi-Specific DARPin Potently Neutralizes Shiga Toxin 2 via Simultaneous Modulation of Both Toxin Subunits. Authors: Yu Zeng / Mengqiu Jiang / Sally Robinson / Zeyu Peng / Vikas Chonira / Rudo Simeon / Saul Tzipori / Junjie Zhang / Zhilei Chen / ![]() Abstract: Shiga toxin-producing (STEC) is a common cause of bloody diarrhea. The pathology of STEC infection derives from two exotoxins-Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2)-that are secreted by STEC ...Shiga toxin-producing (STEC) is a common cause of bloody diarrhea. The pathology of STEC infection derives from two exotoxins-Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2)-that are secreted by STEC in the gut, from where they are systemically absorbed, causing severe kidney damage leading to hemolytic uremic syndrome (HUS). Currently, there is no effective treatment for HUS, and only supportive care is recommended. We report the engineering of a panel of designed ankyrin repeat proteins (DARPin) with potent neutralization activity against Stx2a, the major subtype associated with HUS. The best dimeric DARPin, SD5, created via a combination of directed evolution and rational design, neutralizes Stx2a with a half maximal effective concentration (EC) of 0.61 nM The two monomeric DARPin constituents of SD5 exhibit complementary functions-SHT targets the enzymatic A subunit of Stx2a and inhibits the toxin's catalytic activity, while DARPin #3 binds the B subunit, based on the cryo-EM study, and induces a novel conformational change in the B subunit that distorts its five-fold symmetry and presumably interferes with toxin attachment to target cells. SD5 was fused to an albumin-binding DARPin, and the resulting trimeric DARPin DA1-SD5 efficiently protects mice in a toxin challenge model, pointing to a high potential of this DARPin as a therapeutic for STEC infection. Finally, the unprecedented toxin conformational change induced by DARPin #3 represents a novel mode of action for neutralizing Stx2 toxicity and reveals new targets for future drug development. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 204.2 KB | Display | ![]() |
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PDB format | ![]() | 162.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438 KB | Display | ![]() |
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Full document | ![]() | 470.5 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26563MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 1 molecules G
#1: Protein | Mass: 19863.410 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synthetic construct (others) Production host: ![]() |
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-Shiga-like toxin 2 subunit ... , 2 types, 6 molecules ABCDEF
#2: Protein | Mass: 33228.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: P09385, rRNA N-glycosylase |
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#3: Protein | Mass: 7824.590 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() References: UniProt: P09386 |
-Non-polymers , 5 types, 540 molecules ![](data/chem/img/1PS.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-1PS / #5: Chemical | ChemComp-FMT / #6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-EDO / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108744 / Symmetry type: POINT |